Hi Pathfinder,
Seems really strange to me. Do you have their confirmation email - I mean, 'your app is complete and ready for consideration'? If so, and if the date of this email is before the deadline, I believe you could use it as a proof.
However, it may well be that your recommenders indeed sumbitted their letters on 9/30 but the delivery was postponed because of some technical issues. In this case, I believe it's just bad luck.
I doubt that JBS will be using some special tricks just in order to move somebody to R1.5. Seems just like technical or organisational problem. I believe they received much more apps in R1 than they had been expecting.
Anyways, good luck for R1.5! It's just my feeling, of course, but it is possible that 1.5 won't be that bad. Now I see that many applicants pushed themselves into R1 when they saw this additional round, so the competition in R1.5 may be not as strong. I believe that you, Teutonic and Lumone have good chances.
BTW, how about your plans for LBS?